feat2-0, no concatenation of fastqs

[MartiPedna]

I am running the feat2-0 branch version of the pipeline. I give the same sample and group names to 2 fastq files in order to concatenate them. This doesn't happen and the 2 samples are treated separately. The pipeline fails at Process NFCORE_CLIPSEQ:CLIPSEQ:CONSENSUS_CROSSLINKS_CAT_CAT as there is collision between the sample names.

Steps to reproduce

Steps to reproduce the behaviour:

Command line: ../clipseq/main.nf -c KCL-CREATE_interruptible.config --input samplesheet.csv
--source "fastq" --fasta "Homo_sapiens.GRCh38.fasta" --gtf "Homo_sapiens.GRCh38.109.gtf" --ncrna_fasta "Homo_sapiens.GRCh38.smrna.fasta"

##Error

ERROR ~ Error executing process > 'NFCORE_CLIPSEQ:CLIPSEQ:CONSENSUS_CROSSLINKS_CAT_CAT'

Caused by:
Process NFCORE_CLIPSEQ:CLIPSEQ:CONSENSUS_CROSSLINKS_CAT_CAT input file name collision -- There are multiple input files for each of the following file names: input3.genome.xl.bed

##Samplesheet:
sample_name,group_name,input_name,fastq IP_R3_T1,IP,input,../ultraplex_demux_WT_C_20230124_Fwd.fastq.gz IP_R4_T1,IP,input,../ultraplex_demux_WT_D_20230124_Fwd.fastq.gz input2,input,,../ultraplex_demux_input_SP3_temp_WT_B_20230124_Fwd.fastq.gz input3,input,,../ultraplex_demux_input_SP3_temp_WT_C_20230124_Fwd.fastq.gz input3,input,,../ultraplex_demux_input_SP3_temp_WT_D_20230124_Fwd.fastq.gz

System

• Hardware: HPC
• Executor: slurm
• Engine: Singularity

[iraiosub]

Hi Martina,
I had a quick look through the main workflow and subworkflows, and as far as I can see the pipeline doesn’t currently support concatenation of FASTQs based on the samplesheet (each line becomes its own sample, and the CAT_FASTQ module isn't used). The usage docs look like boilerplate from the nf-core template (similar to nf-core/rnaseq), so they’re probably not yet up to date with the actual implementation. Concatenation would definitely be a helpful feature to add.